The Senior Salaries Review Board recommended the pay increase in a recent report, but the government has decided not to make it a uniform pay rise, instead giving departments the flexibility to determine whether and how to pay the increase.
The government did accept recommendations that senior civil service salary minima be increased from 1 April 2014 to £62,000 for Pay Band 1, £85,000 for Pay Band 2 and £104,000 for Pay Band 3.
It said it will consider recommendations to increase permanent secretary pay minima by £1,500 to £143,500 for Tier 3, £161,500 for Tier 2 and £181,500 for Tier 1.
The FDA has criticised the government's move. FDA general secretary Dave Penman said: "The Government are putting at risk the future capability of the civil service by refusing to reform pay.
“Once again the Government have ignored the evidence that shows huge long-term dissatisfaction with pay and a widening chasm between civil service pay levels and the rest of the economy.
"It is no longer the case that they are sleep walking into a disaster; the SSRB itself, the National Audit Office, the Civil Service Commission, the Public Administration Select Committee and the FDA have all highlighted evidence of growing discontent and the need for longer term reform."